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  • 1
    Electronic Resource
    Electronic Resource
    An all-atom empirical energy function for the simulation of nucleic acids (1995)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 117 (1995), S. 11946-11975 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00153a017
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  • 2
    Electronic Resource
    Electronic Resource
    Pathways for Conformational Interconversion of Calix[4]arenes (1995)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 117 (1995), S. 1611-1620 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00110a017
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  • 3
    Electronic Resource
    Electronic Resource
    Simulations of Macromolecules by Multiple Time-Step Methods (1995)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 5680-5697 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100015a061
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  • 4
    Electronic Resource
    Electronic Resource
    Interpreting the folding kinetics of helical proteins (1999)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 401 (1999), S. 400-403 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The detailed mechanism of protein folding is one of the major problems in structural biology. Its solution is of practical as well as fundamental interest because of its possible role in utilizing the many sequences becoming available from genomic analysis. Although the Levinthal paradox ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/401400a0
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  • 5
    Electronic Resource
    Electronic Resource
    Simulation of activation free energies in molecular systems (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 1902-1921 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A method is presented for determining activation free energies in complex molecular systems. The method relies on knowledge of the minimum energy path and bases the activation free energy calculation on moving along this path from a minimum to a saddle point. Use is made of a local reaction coordinate which describes the advance of the reaction in each segment of the minimum energy path. The activation free energy is formulated as a sum of two terms. The first is due to the change in the local reaction coordinate between the endpoints of each segment of the path. The second is due to the change in direction of the minimum energy path between consecutive segments. Both contributions can be obtained by molecular dynamics simulations with a constraint on the local reaction coordinate. The method is illustrated by applying it to a model potential and to the C7eq to C7ax transition in the alanine dipeptide. It is found that the term due to the change of direction in the reaction path can make a substantial contribution to the activation free energy. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472061
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  • 6
    Electronic Resource
    Electronic Resource
    Orientational correlations and entropy in liquid water (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 4294-4316 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The molecular pair correlation function in water is a function of a distance and five angles. It is here separated into the radial distribution function (RDF), which is only a function of distance, and an orientational distribution function (ODF), which is a function of the five angles for each distance between the molecules. While the RDF can be obtained from computer simulations, this is not practical for the ODF due to its high dimensionality. Two approaches for obtaining an approximation to the ODF are introduced. The first uses a product of one- and two-dimensional marginal distributions from computer simulations. The second uses the gas-phase low-density limit as a reference and applies corrections based on (a) the orientationally averaged interactions in the liquid calculated by simulations, and (b) the observed differences in the one- and two-dimensional marginal distributions in the gas and in the liquid. The site superposition approximation was also tested and found to be inadequate for reproducing the orientationally averaged interaction energy and the angular distributions obtained from the simulations. The two approximations to the pair correlation function are employed to estimate the contribution of two-particle correlations to the excess entropy of TIP4P water. The calculated value is comparable to the excess entropy of TIP4P water estimated by other methods and to the experimental excess entropy of liquid water. More than 90% of the orientational part of the excess entropy is due to correlations between first neighbors. The change in excess entropy with temperature gives a value for the heat capacity that agrees within statistical uncertainty with that obtained from the change in energy with temperature and is reasonably close to the experimental value for water. The effect of pressure on the entropy was examined and it was found that increase in the pressure (density) causes a reduction of orientational correlations, in agreement with the idea of pressure as a "structure breaker'' in water. The approach described here provides insight concerning the nature of the contributions to the excess entropy of water and should be applicable to other simple molecular fluids. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472247
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  • 7
    Electronic Resource
    Electronic Resource
    Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 107 (1997), S. 10691-10708 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The thermodynamics of homopolymers and clusters with square-well interactions of up to 64 particles are studied with constant-temperature discontinuous molecular dynamics (DMD) simulations; for comparison Monte Carlo (MC) simulations are also reported. Homopolymers composed of more than five beads are found to exhibit two or more equilibrium transitions. In the long chain limit, these multiple transitions correspond to gas-to-liquid, liquid-to-solid, and solid-to-solid transitions. In particular, the liquid-to-solid-like disorder-to-order transition for isolated 32mers and 64mers is strongly first order (bimodal energy distribution) at the reduced square-well diameter λ=1.5. As λ decreases from 1.5 to 1.3, the bimodal distribution becomes unimodal. The use of Lindemann's rule for solids indicates that the structure formed right below the liquid-to-solid transition temperature has a solid core but a liquid surface. Comparing the homopolymer results with those for square-well clusters indicates that the bonding constraint in homopolymers increases the temperatures of transitions but decreases their strength. The solid structure of an isolated 64mer is nearly identical to that of a cluster of 64 beads. Possible approaches to the experimental observation of the solid-state for an isolated chain are discussed. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.474186
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  • 8
    Electronic Resource
    Electronic Resource
    A position dependent friction model for solution reactions in the high friction regime: Proton transfer in triosephosphate isomerase (TIM) (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 10812-10818 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A position dependent friction model based on Grote–Hynes theory is developed to describe activated rate processes in the high friction regime. The model is employed to determine the transmission coefficient, which corrects the transition state theory rate constant for recrossing of the transition state. A simple expression is derived for the transmission coefficient in the limit of a slow response of the thermal bath. The model is applied to the initial proton transfer step in the reaction catalyzed by triosephosphate isomerase, for which the standard Grote–Hynes theory was found to be inappropriate. The predictions of the position dependent friction model are in a good agreement with results of detailed molecular dynamics simulations. The method used to determine the transmission coefficient should be generally applicable to reactions that are strongly coupled to a slow thermal bath. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472889
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  • 9
    Electronic Resource
    Electronic Resource
    The Jacobian factor in free energy simulations (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 5145-5154 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The role of Jacobian factors in free energy simulations is described. They provide a simple interpretation of "moment of inertia correction'' and "dynamic stretch free energy'' terms in such simulations. Since the relevant Jacobian factors can often be evaluated analytically by use of the configurational partition function of a polyatomic molecule, it is possible to subtract them from the simulation results when they make unphysical contributions. An important case arises in alchemical simulations that use a single topology method and introduce dummy particles to have the same number of atoms in the initial and final state. The more general utility of the Jacobian factors for simulations of complex systems is briefly discussed. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472358
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  • 10
    Electronic Resource
    Electronic Resource
    Temperature quench echoes in proteins (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 3112-3123 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Temperature quench echoes are analyzed in terms of the temperature–temperature correlation function in the harmonic approximation, and the resulting expressions are compared with molecular dynamics simulations. The relationship between the time dependence of the echo depth and the density of states is demonstrated for harmonic systems. For a protein, which has significant anharmonicity, the time dependence is dominated by relaxation effects that originate from dephasing of the periodic motions. A simple relaxation model is shown to provide a good description of the results observed in the simulations. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470270
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